/EXTERNAL BLUEPRINT/variants/K006271_11_lane_gembs
BACK
SAMPLE K006271_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1136888807 |
716210742 |
63.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1136888807 |
100% |
1121504422 |
98.65 % |
15384385 |
1.35 % |
| |
|
|
|
|
|
|
| Passed |
718354239 |
63.19 % |
714673553 |
63.72 % |
3680686 |
0.51 % |
| Filtered |
418534568 |
36.81 % |
406830869 |
36.28 % |
11703699 |
1.63 % |
| |
|
|
|
|
|
|
| q20 |
357843673 |
85.50 % |
356036066 |
87.51 % |
1807607 |
15.44 % |
| q20,qd2 |
34174660 |
8.17 % |
24867206 |
6.11 % |
9307454 |
79.53 % |
| q20,mq40 |
14412630 |
3.44 % |
14314199 |
3.52 % |
98431 |
0.84 % |
| mq40 |
6511170 |
1.56 % |
6323745 |
1.55 % |
187425 |
1.60 % |
| q20,qd2,mq40 |
3109909 |
0.74 % |
2931749 |
0.72 % |
178160 |
1.52 % |
| qd2 |
2397290 |
0.57 % |
2289345 |
0.56 % |
107945 |
0.92 % |
| qd2,mq40 |
79919 |
0.02 % |
68559 |
0.02 % |
11360 |
0.10 % |
| q20,qd2,fs60 |
1345 |
0.00 % |
0 |
0.00 % |
1345 |
0.01 % |
| qd2,fs60,mq40 |
1255 |
0.00 % |
0 |
0.00 % |
1255 |
0.01 % |
| fs60 |
900 |
0.00 % |
0 |
0.00 % |
900 |
0.01 % |
| qd2,fs60 |
778 |
0.00 % |
0 |
0.00 % |
778 |
0.01 % |
| fs60,mq40 |
568 |
0.00 % |
0 |
0.00 % |
568 |
0.00 % |
| q20,qd2,fs60,mq40 |
471 |
0.00 % |
0 |
0.00 % |
471 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
3938995 |
22.56 % |
| Transition |
G>A |
All |
3358134 |
19.23 % |
| Transition |
T>C |
All |
3884566 |
22.25 % |
| Transition |
C>T |
All |
3492396 |
20.00 % |
| Transversion |
A>C |
All |
215913 |
1.24 % |
| Transversion |
C>A |
All |
545427 |
3.12 % |
| Transversion |
T>G |
All |
221426 |
1.27 % |
| Transversion |
G>T |
All |
530836 |
3.04 % |
| Transversion |
A>T |
All |
439675 |
2.52 % |
| Transversion |
T>A |
All |
430602 |
2.47 % |
| Transversion |
C>G |
All |
203894 |
1.17 % |
| Transversion |
G>C |
All |
197966 |
1.13 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
445351 |
19.47 % |
| Transition |
G>A |
Passed |
379759 |
16.61 % |
| Transition |
T>C |
Passed |
422572 |
18.48 % |
| Transition |
C>T |
Passed |
377672 |
16.51 % |
| Transversion |
A>C |
Passed |
87087 |
3.81 % |
| Transversion |
C>A |
Passed |
81941 |
3.58 % |
| Transversion |
T>G |
Passed |
87023 |
3.81 % |
| Transversion |
G>T |
Passed |
81353 |
3.56 % |
| Transversion |
A>T |
Passed |
60253 |
2.63 % |
| Transversion |
T>A |
Passed |
60548 |
2.65 % |
| Transversion |
C>G |
Passed |
101603 |
4.44 % |
| Transversion |
G>C |
Passed |
101839 |
4.45 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
5.27 |
14674091 |
2785739 |
| Passed |
2.46 |
1625354 |
661647 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |